Repeated antibiotics alter beneficial gut germs

Antibiotics can temporarily upset your stomach, but now it turns out that repeatedly taking them can trigger long-lasting changes in all those good germs that live in your gut, raising questions about lingering ill effects.

Nobody yet knows if that leads to later health problems. But the finding is the latest in a flurry of research raising questions about how the customized bacterial zoo that thrives in our intestines forms — and whether the wrong type or amount plays a role in ailments from obesity to inflammatory bowel disease to asthma.

Don't be grossed out: This is a story in part about, well, poop. Three healthy adults collected weeks of stool samples so that scientists could count exactly how two separate rounds of a fairly mild antibiotic caused a surprising population shift in their microbial netherworld — as some original families of germs plummeted and other types moved in to fill the gap.

It's also a story of how we coexist with trillions of bacteria, fungi and other microbes in the skin, the nose, the digestive tract, what scientists call the human microbiome. Many are beneficial, even indispensable, especially the gut bacteria that play an underappreciated role in overall health.

"Gut communities are fundamentally important in the development of our immune system," explains Dr. David Relman of Stanford University, who led the antibiotic study published Monday in Proceedings of the National Academy of Sciences. "Let's not take them for granted."

Next, Relman plans to track if antibiotics during the first or two year of life, when youngsters form what will become their unique set of gut bacteria, seem to predispose children to later immune-related diseases.